Merck’s HPV vaccine, Gardasil, was found to be safe in a large safety study required by the Food and Drug Administration (FDA).

The vaccine did cause fainting on the day of the shot and skin infections two weeks later in some women — known short-term side effects of the vaccine. It was not associated with serious health effects.

Gardasil protects against four strains of the sexually transmitted HPV, or human papillomavirus, two of which are the leading cause of cervical cancer in women. HPV is also linked with genital warts, vaginal cancer and, in men, oral cancers. Most HPV infections, with lower-risk strains, will usually clear on their own within two years, however.

Merck’s vaccine was first approved by the FDA in 2006 for girls and women ages 9 to 26, and is now approved also for boys and men. Federal vaccine guidelines recommend the three-dose for boys and girls before they become sexually active, around age 11 or 12. Follow-up studies such as this one are the norm to highlight any potentially overlooked side effects of widely-used drugs or vaccines.

The new study, published in the journal Archives of Pediatrics & Adolescent Medicine, researchers looked at the medical records of 189,629 girls and women ages 9 to 26 within the Northern and Southern California Kaiser Permanente health care systems. All the women received at least one dose of Gardasil between August 2006 and March 2008. By the end of the study period, 44,000 participants had received the recommended three doses of the vaccine.

The researchers examined the rate of emergency department visits and hospitalizations for women in the two weeks following their vaccination and again a couple months later. Aside from some episodes of fainting and skin infections, the authors found no other safety concerns. There were some reports of seizures and allergic reactions, but a five-member safety committee of medical experts with no ties to the Kaiser study team or Merck and Co., which funded the study, concluded that these reactions were not related to the vaccine.

The authors noted that some skin infections could simply be swelling at the injection site, a possible short-term reaction that is included in the vaccine’s safety information. Further, fainting is a somewhat common side effect of vaccines in general, not just the HPV vaccine, the authors said. “We think this is a very reassuring study,” says study author Dr. Nicola Klein of the Kaiser Permanente Vaccine Study Center in Oakland, Calif. “We looked at many women and girls and found no safety concerns.”

The CDC also recommends the HPV vaccine for girls and women through age 26 and boys and men through age 21, if they did not receive all three doses of the vaccine when they were younger.